Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013374.1 Corchorus olitorius cultivar O-4 contig13407, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 16241
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:900 original size:29 final size:29

Alignment explanation


    Indices: 868--924  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        858 TATGTATGAC

                        *                
        868 TTTTTGAGATAACTAATTAATATGACTTA
          1 TTTTTGAGATAAATAATTAATATGACTTA

                 *                      
        897 TTTTTTAGATAAATAATTAATATGACTT
          1 TTTTTGAGATAAATAATTAATATGACTT

        925 TATATTTCTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47


Consensus pattern (29 bp):   
TTTTTGAGATAAATAATTAATATGACTTA

Found at i:1812 original size:16 final size:16

Alignment explanation


    Indices: 1773--1817  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1763 TAATTTAGAG

                  *    *    
       1773 GGAATTAAATTGAGAA
          1 GGAATTGAATTAAGAA

                            
       1789 GGAATTGAATTAAGAA
          1 GGAATTGAATTAAGAA

               *         
       1805 GGATTTGAATTAA
          1 GGAATTGAATTAA

       1818 CAATTACATA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29


Consensus pattern (16 bp):   
GGAATTGAATTAAGAA

Found at i:7703 original size:6 final size:6

Alignment explanation


    Indices: 7682--7715  Score: 50
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       7672 AACATGTTAA

                       **                          
       7682 TTTTCT TTTTAG TTTTCT TTTTCT TTTTCT TTTT
          1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT

       7716 AGGATTCCAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82


Consensus pattern (6 bp):   
TTTTCT

Found at i:8631 original size:18 final size:17

Alignment explanation


    Indices: 8599--8634  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       8589 AAAGGGTAGT

                    *        
       8599 TAAAAAAATTGTTTTCA
          1 TAAAAAAAGTGTTTTCA

                              
       8616 TAAAACAAAGTGTTTTCA
          1 TAAAA-AAAGTGTTTTCA

             
       8634 T
          1 T

       8635 GCAAGAGGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    5  0.29
  18   12  0.71

ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39


Consensus pattern (17 bp):   
TAAAAAAAGTGTTTTCA

Found at i:12271 original size:91 final size:91

Alignment explanation


    Indices: 12116--12298  Score: 366
    Period size: 91  Copynumber: 2.0  Consensus size: 91

      12106 GAAATAAGTG

                                                                             
      12116 TGGGGGAATGTTTCTCACTAAAGCTTCCATAGACACCTTAATTTTAAACCCACTTCTTTAATATC
          1 TGGGGGAATGTTTCTCACTAAAGCTTCCATAGACACCTTAATTTTAAACCCACTTCTTTAATATC

                                      
      12181 CCCGCATTTTCCTTCTTAGGTCATAT
         66 CCCGCATTTTCCTTCTTAGGTCATAT

                                                                             
      12207 TGGGGGAATGTTTCTCACTAAAGCTTCCATAGACACCTTAATTTTAAACCCACTTCTTTAATATC
          1 TGGGGGAATGTTTCTCACTAAAGCTTCCATAGACACCTTAATTTTAAACCCACTTCTTTAATATC

                                      
      12272 CCCGCATTTTCCTTCTTAGGTCATAT
         66 CCCGCATTTTCCTTCTTAGGTCATAT

             
      12298 T
          1 T

      12299 CCTTTAGCCA


Statistics
Matches: 92,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  91   92  1.00

ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38


Consensus pattern (91 bp):   
TGGGGGAATGTTTCTCACTAAAGCTTCCATAGACACCTTAATTTTAAACCCACTTCTTTAATATC
CCCGCATTTTCCTTCTTAGGTCATAT
Done.